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QM/MM Simulation


Hybrid quantum mechanics/molecular mechanics (QM/MM) simulation has become a powerful tool for investigating chemical reactions in condensed phases. QM/MM simulation based on classical mechanics and quantum mechanics is considered to be one of the most reliable computational simulation methods for studying many chemical reaction mechanisms, especially when combined with molecular dynamics simulation (MD). In the QM/MM method, the chemical process takes place is treated at an appropriate level of quantum chemistry theory, while the remainder is described by a molecular mechanics force field.

QM and MM SimulationFigure 1. a) QM/MM model with bulk water molecules (left) and QM region(right) used in this study. b) Final snapshots (DR, ZW, EP) from the QM/MMMD equilibration exploited as the initial configurations for ABF simulations,with isovalue surfaces of positive (orange) and negative (yellow) spin density (isovalue=0.01). The RLC-BLYP/6-31G* method was used for ZW and EP, and the BS-ULC-BLYP/6-31G* method was used for DR. (Saito, T.; Takano, Y. 2021)

Our Process

1. Create 3D molecules and prepare topology and 3D coordinate files required for calculations.

2. Select basis set type to be used in the calculation such as STO-3G, 3-21G, 6-31G and 6-311.

3. Select optimal method to be used in the calculation such as RHF or MP2, or some supported DFT functional. Popular choices are BLYP, PBE and B3LYP.

4. Output coordinate file of atom.

5. Calculate the energy.

Our Services

At Alfa Chemistry, we have designed a QM/MM simulation method to study a series of structural and energy changes involved in the reaction process at the atomic and electronic level. In addition, our well-developed QM/MM simulation can help to investigate the reaction mechanism. Our fast and high-quality services include the following:

  • We use QM/MM MD simulation to help to deeply understand a series of key information such as the structure and energy changes involved in the enzyme reaction process from the atomic and electronic level.

  • We performed free energy (PMF) simulations based on QM/MM MD simulation, pKa calculation, and the statistical analysis such as the ANOVA test to investigate the catalytic mechanism.

  • Our experts have designed QM/MM (DFTB3/CHARMM36) MD simulations, in which the atoms included in QM region are described by the third-order self-consistent charge density functional tight-binding (DFTB3, 3ob-2-1) method and the MM atoms are described by the classical CHARMM36 force field. The binding properties of different complexes are able to be revealed.

  • We can also apply the QM/MM potential energy surface combined with the Feynman path integral-free energy perturbation theory (PI-FEP) to calculate the equilibrium isotope effect (EIE) in the solution system and the isotope fractionation factor (IFF).

  • Our teams can also use QM/MM multi-scale biomacromolecule molecular dynamics simulation method to study the changes in the electronic structure of the receptor and ligand during the binding process. Important information on the specificity of molecular recognition and binding can be obtained, which allows for further study of the mechanism of molecular interaction recognition and binding.

Application of Our Services

  • Study the mechanism of enzyme catalysis, often including transition state process.
  • Study the proton transfer and charge transfer reaction process.
  • Study the Induced luminescence mechanism.

Our Capabilities

  • Optimization type

Minimum energy
Transition state

  • Kinetic type

Ground state simulation
Excited state simulation
Intersystem jump: simulate the transition from excited state to ground state

  • QM/MM boundary type

Standard QM/MM model
ONIOM model
Multi-layer ONIOM model

Why Choose Us?

  • At Alfa Chemistry, multiple optimization type, kinetic type and QM/MM boundary type are available.
  • We have considerable practical experience and core technology in QM/MM simulation, aiming to provide high-quality technical services for you.

QM/MM simulation provides an effective way to optimize the chemical process. Our QM/MM simulation services remarkably reduce the cost, promote further experiments, and enhance the understanding of chemical process for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Saito, T.; Takano, Y. Spin-projected QM/MM Free Energy Simulations for Oxidation Reaction of Guanine in B-DNA by Singlet Oxygen. ChemPhysChem. 2021, 22(6): 561-568.

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